Convergence of Sampling and Deciding on Simulation Length

From: Aditya Ranganathan (
Date: Tue Jul 16 2013 - 06:08:15 CDT

Hello All,

With the ability to run simulations over long timescales and all the
analysis with all the Essential Dynamics and Normal Mode Analysis tools
that we have available to us now, I have a fundamental question to ask. How
do we decide whether our simulation has run long enough for the PCA and EMD
analysis to be of any relevance? For example, cosine content of a
trajectory (Physical Rev. E. Vol 65, 031910) that can be calculated in
Gromacs seems to be reported as one of the measures of understanding the
contribution of diffusion to the protein motion during the simulation. Is
there a way to calculate cosine content in VMD/NAMD? Also, are there other
parameters which one should look at while trying to decide if the
simulation has run long enough to give meaningful results and not noise.
How do we check for convergence?

Thanks and Regards

Srivastav Ranganathan

Research Scholar
Department of Biosciences and Bioengineering,
IIT Bombay

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